PDBsum entry 1xf3

Immune system

PDB id: 1xf3

Contents

Protein chains

213 a.a. *

216 a.a. *

Waters ×66

* Residue conservation analysis

PDB id:

1xf3

Name:

Immune system

Title:

Structure of ligand-free fab DNA-1 in space group p65

Structure:

Fab light chain. Chain: l, a. Engineered: yes. Fab heavy chain. Chain: h, b. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.210 R-free: 0.243

Authors:

J.P.Schuermann,S.P.Prewitt,S.L.Deutscher,J.J.Tanner

Key ref:

J.P.Schuermann et al. (2005). Evidence for structural plasticity of heavy chain complementarity-determining region 3 in antibody-ssDNA recognition. J Mol Biol, 347, 965-978. PubMed id: 15784256 DOI: 10.1016/j.jmb.2005.02.008

Date:

13-Sep-04 Release date: 12-Apr-05

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 216 a.a.

DOI no: 10.1016/j.jmb.2005.02.008

J Mol Biol 347:965-978 (2005)

PubMed id: 15784256

Evidence for structural plasticity of heavy chain complementarity-determining region 3 in antibody-ssDNA recognition.

J.P.Schuermann, S.P.Prewitt, C.Davies, S.L.Deutscher, J.J.Tanner.

ABSTRACT

Anti-DNA antibodies play important roles in the pathogenesis of autoimmune diseases. They also represent a unique and relatively unexplored class of DNA-binding protein. Here, we present a study of conformational changes induced by DNA binding to an anti-ssDNA Fab known as DNA-1. Three crystal structures are reported: a complex of DNA-1 bound to dT3, and two structures of the ligand-free Fab. One of the ligand-free structures was determined from crystals exhibiting perfect hemihedral twinning, and the details of structure determination are provided. Unexpectedly, five residues (H97-H100A) in the apex of heavy chain complementarity-determining region 3 (HCDR3) are disordered in both ligand-free structures. Ligand binding also caused a 2-4A shift of the backbone of Tyr L92 and ordering of the L92 side-chain. In contrast, these residues are highly ordered in the Fab/dT3 complex, where Tyr H100 and Tyr H100A form intimate stacking interactions with DNA bases, and L92 forms the 5' end of the binding site. The structures suggest that HCDR3 is very flexible and adopts multiple conformations in the ligand-free state. These results are discussed in terms of induced fit and pre-existing equilibrium theories of ligand binding. Our results allow new interpretations of existing thermodynamic and mutagenesis data in terms of conformational entropy and the volume of conformational space accessible to HCDR3 in the ligand-free state. In the context of autoimmune disease, plasticity of the ligand-free antibody could provide a mechanism by which anti-DNA antibodies bind diverse host ligands, and thereby contribute to pathogenicity.

Selected figure(s)

Figure 2.
Figure 2. Stereo-view of the dT[3] binding site. The protein is white; DNA is colored yellow. A s[A]-weighted mF[o] -DF[c] electron density map is shown in blue (3s). The dT[3] ligand and surrounding residues within 3.9 Å were omitted prior to simulated annealing refinement and map calculation. Shown in pink is an anomalous difference Fourier map (2.5s) calculated from data collected using CuK[a] radiation.

Figure 6.
Figure 6. Stereo-views of heavy chain residues 93-102 from the two ligand-free structures, which includes HCDR3. For reference, the sequence of heavy chain residues 93-102 is 93VRGGYRP100Y100AY100BA^100CMD^102Y. (a) HCDR3 from Fab 2 of the P6[5] structure. (b) HCDR3 from Fab 1 of the P321 structure. The electron density maps for both panels are simulated annealing s[A]-weighted mF[o] -DF[c] maps and the contour level is 3s. Prior to map calculation, heavy chain residues 94-101, along with surrounding residues within 3.9 Å, were omitted from the model and simulated annealing was performed. Note that residues 98-100A (RPYY) are disordered, and they appear in the deposited PDB entries with occupancy of zero. A theoretical model of the backbone of residues 98-100A is drawn to help guide the eye.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 347, 965-978) copyright 2005.

Figures were selected by the author.